1RZG | pdb_00001rzg

Crystal structure of Human anti-HIV-1 GP120 reactive antibody 412d

PDB DOI: https://doi.org/10.2210/pdb1RZG/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: human gammaherpesvirus 4
Mutation(s): No

Deposited: 2003-12-24 Released: 2004-02-03
Deposition Author(s): Huang, C.C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.-Y., Dimitrov, D.S., Hendrickson, W.A., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.253 (DCC)
R-Value Work:
0.201 (Depositor), 0.206 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120

Huang, C.C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.-Y., Dimitrov, D.S., Hendrickson, W.A., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D.

(2004) Proc Natl Acad Sci U S A 101: 2706-2711

PubMed: 14981267 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0308527100
Primary Citation Related Structures:
1RZ7, 1RZ8, 1RZF, 1RZG, 1RZI, 1RZJ, 1RZK

PubMed Abstract:
The conserved surface of the HIV-1 gp120 envelope glycoprotein that binds to the HIV-1 coreceptor is protected from humoral recognition by multiple layers of camouflage. Here we present sequence and genomic analyses for 12 antibodies that pierce these defenses and determine the crystal structures of 5. The data reveal mechanisms and atomic-level details for three unusual immune features: posttranslational mimicry of coreceptor by tyrosine sulfation of antibody, an alternative molecular mechanism controlling such sulfation, and highly selective V(H)-gene usage. When confronted by extraordinary viral defenses, the immune system unveils novel adaptive capabilities, with tyrosine sulfation enhancing the vocabulary of antigen recognition.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 99.14 kDa
Atom Count: 7,395
Modeled Residue Count: 865
Deposited Residue Count: 890
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 412d light chain	A, C	231	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 412d heavy chain	B, D	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F, G, H, I E, F, G, H, I, J, K	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
CYS Query on CYS Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	A, C	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	E, F, G, H, I E, F, G, H, I, J, K	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.253 (DCC)
R-Value Work: 0.201 (Depositor), 0.206 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.088	α = 90
b = 89.313	β = 110.31
c = 85.863	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-02-03
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary